Mon 24 Dec 00:46:27 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2a2m-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2a2m-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2a2m-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a2m-3.8-parrot-mrncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a2m-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a2m-3.8-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 00:46:32 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a2m-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a2m-3.8-parrot-mrncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 595 and 0 Target number of residues in the AU: 595 Target solvent content: 0.6601 Checking the provided sequence file Detected sequence length: 258 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 516 Adjusted target solvent content: 0.71 Input MTZ file: 2a2m-3.8-parrot-mrncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 209 Cell parameters: 283.292 283.292 283.292 90.000 90.000 90.000 Input sequence file: 2a2m-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4128 target number of atoms Had to go as low as 0.95 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 163.559 3.801 Wilson plot Bfac: 84.92 10076 reflections ( 99.70 % complete ) and 0 restraints for refining 4587 atoms. Observations/parameters ratio is 0.55 ------------------------------------------------------ Starting model: R = 0.3392 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3322 (Rfree = 0.000) for 4587 atoms. Found 25 (25 requested) and removed 36 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.59 2.66 Search for helices and strands: 0 residues in 0 chains, 4708 seeds are put forward NCS extension: 0 residues added, 4708 seeds are put forward Round 1: 284 peptides, 44 chains. Longest chain 23 peptides. Score 0.390 Round 2: 309 peptides, 39 chains. Longest chain 19 peptides. Score 0.472 Round 3: 317 peptides, 38 chains. Longest chain 19 peptides. Score 0.492 Round 4: 316 peptides, 37 chains. Longest chain 28 peptides. Score 0.498 Round 5: 314 peptides, 37 chains. Longest chain 20 peptides. Score 0.495 Taking the results from Round 4 Chains 38, Residues 279, Estimated correctness of the model 0.0 % 1 chains (23 residues) have been docked in sequence ------------------------------------------------------ 10076 reflections ( 99.70 % complete ) and 7977 restraints for refining 3733 atoms. 6815 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2805 (Rfree = 0.000) for 3733 atoms. Found 20 (20 requested) and removed 21 (10 requested) atoms. Cycle 2: After refmac, R = 0.2694 (Rfree = 0.000) for 3658 atoms. Found 20 (20 requested) and removed 29 (10 requested) atoms. Cycle 3: After refmac, R = 0.2647 (Rfree = 0.000) for 3616 atoms. Found 20 (20 requested) and removed 19 (10 requested) atoms. Cycle 4: After refmac, R = 0.2614 (Rfree = 0.000) for 3594 atoms. Found 19 (19 requested) and removed 25 (9 requested) atoms. Cycle 5: After refmac, R = 0.2467 (Rfree = 0.000) for 3568 atoms. Found 19 (19 requested) and removed 31 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.58 2.66 Search for helices and strands: 0 residues in 0 chains, 3757 seeds are put forward NCS extension: 31 residues added (2 deleted due to clashes), 3788 seeds are put forward Round 1: 313 peptides, 35 chains. Longest chain 19 peptides. Score 0.508 Round 2: 314 peptides, 31 chains. Longest chain 25 peptides. Score 0.538 Round 3: 310 peptides, 27 chains. Longest chain 27 peptides. Score 0.561 Round 4: 312 peptides, 31 chains. Longest chain 29 peptides. Score 0.535 Round 5: 319 peptides, 30 chains. Longest chain 25 peptides. Score 0.553 Taking the results from Round 3 Chains 31, Residues 283, Estimated correctness of the model 0.0 % 4 chains (38 residues) have been docked in sequence ------------------------------------------------------ 10076 reflections ( 99.70 % complete ) and 7782 restraints for refining 3731 atoms. 6535 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2605 (Rfree = 0.000) for 3731 atoms. Found 20 (20 requested) and removed 27 (10 requested) atoms. Cycle 7: After refmac, R = 0.2517 (Rfree = 0.000) for 3666 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 8: After refmac, R = 0.2490 (Rfree = 0.000) for 3628 atoms. Found 20 (20 requested) and removed 21 (10 requested) atoms. Cycle 9: After refmac, R = 0.2451 (Rfree = 0.000) for 3601 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 10: After refmac, R = 0.2469 (Rfree = 0.000) for 3580 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.61 2.68 Search for helices and strands: 0 residues in 0 chains, 3763 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 3792 seeds are put forward Round 1: 292 peptides, 32 chains. Longest chain 17 peptides. Score 0.498 Round 2: 318 peptides, 33 chains. Longest chain 19 peptides. Score 0.530 Round 3: 320 peptides, 26 chains. Longest chain 30 peptides. Score 0.582 Round 4: 295 peptides, 24 chains. Longest chain 33 peptides. Score 0.561 Round 5: 306 peptides, 24 chains. Longest chain 33 peptides. Score 0.577 Taking the results from Round 3 Chains 29, Residues 294, Estimated correctness of the model 0.0 % 4 chains (58 residues) have been docked in sequence ------------------------------------------------------ 10076 reflections ( 99.70 % complete ) and 7413 restraints for refining 3734 atoms. 6024 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2566 (Rfree = 0.000) for 3734 atoms. Found 20 (20 requested) and removed 24 (10 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 12: After refmac, R = 0.2409 (Rfree = 0.000) for 3690 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 13: After refmac, R = 0.2322 (Rfree = 0.000) for 3650 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 14: After refmac, R = 0.2294 (Rfree = 0.000) for 3623 atoms. Found 19 (20 requested) and removed 21 (10 requested) atoms. Cycle 15: After refmac, R = 0.2282 (Rfree = 0.000) for 3596 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.62 2.69 Search for helices and strands: 0 residues in 0 chains, 3772 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 3799 seeds are put forward Round 1: 300 peptides, 38 chains. Longest chain 20 peptides. Score 0.465 Round 2: 311 peptides, 30 chains. Longest chain 24 peptides. Score 0.541 Round 3: 295 peptides, 29 chains. Longest chain 18 peptides. Score 0.525 Round 4: 305 peptides, 35 chains. Longest chain 21 peptides. Score 0.495 Round 5: 314 peptides, 26 chains. Longest chain 43 peptides. Score 0.574 Taking the results from Round 5 Chains 31, Residues 288, Estimated correctness of the model 0.0 % 4 chains (70 residues) have been docked in sequence ------------------------------------------------------ 10076 reflections ( 99.70 % complete ) and 7110 restraints for refining 3734 atoms. 5697 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2624 (Rfree = 0.000) for 3734 atoms. Found 20 (20 requested) and removed 28 (10 requested) atoms. Cycle 17: After refmac, R = 0.2526 (Rfree = 0.000) for 3660 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 18: After refmac, R = 0.2536 (Rfree = 0.000) for 3623 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 19: After refmac, R = 0.2467 (Rfree = 0.000) for 3603 atoms. Found 17 (19 requested) and removed 17 (9 requested) atoms. Cycle 20: After refmac, R = 0.2319 (Rfree = 0.000) for 3583 atoms. Found 17 (19 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.68 2.73 Search for helices and strands: 0 residues in 0 chains, 3773 seeds are put forward NCS extension: 23 residues added (8 deleted due to clashes), 3796 seeds are put forward Round 1: 301 peptides, 38 chains. Longest chain 26 peptides. Score 0.466 Round 2: 311 peptides, 32 chains. Longest chain 23 peptides. Score 0.527 Round 3: 315 peptides, 31 chains. Longest chain 24 peptides. Score 0.540 Round 4: 313 peptides, 30 chains. Longest chain 23 peptides. Score 0.544 Round 5: 311 peptides, 29 chains. Longest chain 24 peptides. Score 0.548 Taking the results from Round 5 Chains 30, Residues 282, Estimated correctness of the model 0.0 % 4 chains (42 residues) have been docked in sequence ------------------------------------------------------ 10076 reflections ( 99.70 % complete ) and 7785 restraints for refining 3734 atoms. 6495 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2710 (Rfree = 0.000) for 3734 atoms. Found 20 (20 requested) and removed 24 (10 requested) atoms. Cycle 22: After refmac, R = 0.2534 (Rfree = 0.000) for 3682 atoms. Found 20 (20 requested) and removed 21 (10 requested) atoms. Cycle 23: After refmac, R = 0.2468 (Rfree = 0.000) for 3649 atoms. Found 20 (20 requested) and removed 23 (10 requested) atoms. Cycle 24: After refmac, R = 0.2443 (Rfree = 0.000) for 3631 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 25: After refmac, R = 0.2362 (Rfree = 0.000) for 3627 atoms. Found 14 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.65 2.71 Search for helices and strands: 0 residues in 0 chains, 3816 seeds are put forward NCS extension: 40 residues added (1 deleted due to clashes), 3856 seeds are put forward Round 1: 305 peptides, 38 chains. Longest chain 22 peptides. Score 0.473 Round 2: 311 peptides, 35 chains. Longest chain 23 peptides. Score 0.505 Round 3: 295 peptides, 30 chains. Longest chain 28 peptides. Score 0.517 Round 4: 312 peptides, 32 chains. Longest chain 30 peptides. Score 0.528 Round 5: 303 peptides, 28 chains. Longest chain 39 peptides. Score 0.544 Taking the results from Round 5 Chains 31, Residues 275, Estimated correctness of the model 0.0 % 3 chains (41 residues) have been docked in sequence ------------------------------------------------------ 10076 reflections ( 99.70 % complete ) and 7736 restraints for refining 3733 atoms. 6482 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2743 (Rfree = 0.000) for 3733 atoms. Found 20 (20 requested) and removed 25 (10 requested) atoms. Cycle 27: After refmac, R = 0.2588 (Rfree = 0.000) for 3683 atoms. Found 20 (20 requested) and removed 23 (10 requested) atoms. Cycle 28: After refmac, R = 0.2516 (Rfree = 0.000) for 3657 atoms. Found 19 (20 requested) and removed 16 (10 requested) atoms. Cycle 29: After refmac, R = 0.2590 (Rfree = 0.000) for 3646 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 30: After refmac, R = 0.2443 (Rfree = 0.000) for 3636 atoms. Found 13 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.61 2.68 Search for helices and strands: 0 residues in 0 chains, 3826 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 3853 seeds are put forward Round 1: 272 peptides, 39 chains. Longest chain 24 peptides. Score 0.409 Round 2: 302 peptides, 39 chains. Longest chain 21 peptides. Score 0.460 Round 3: 302 peptides, 36 chains. Longest chain 20 peptides. Score 0.483 Round 4: 302 peptides, 36 chains. Longest chain 26 peptides. Score 0.483 Round 5: 305 peptides, 32 chains. Longest chain 23 peptides. Score 0.518 Taking the results from Round 5 Chains 37, Residues 273, Estimated correctness of the model 0.0 % 5 chains (70 residues) have been docked in sequence ------------------------------------------------------ 10076 reflections ( 99.70 % complete ) and 7362 restraints for refining 3734 atoms. 5994 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2685 (Rfree = 0.000) for 3734 atoms. Found 20 (20 requested) and removed 20 (10 requested) atoms. Cycle 32: After refmac, R = 0.2514 (Rfree = 0.000) for 3680 atoms. Found 17 (20 requested) and removed 20 (10 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2493 (Rfree = 0.000) for 3640 atoms. Found 16 (20 requested) and removed 13 (10 requested) atoms. Cycle 34: After refmac, R = 0.2553 (Rfree = 0.000) for 3619 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 35: After refmac, R = 0.2606 (Rfree = 0.000) for 3608 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.67 2.72 Search for helices and strands: 0 residues in 0 chains, 3816 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3836 seeds are put forward Round 1: 259 peptides, 38 chains. Longest chain 12 peptides. Score 0.394 Round 2: 301 peptides, 35 chains. Longest chain 26 peptides. Score 0.489 Round 3: 294 peptides, 31 chains. Longest chain 22 peptides. Score 0.508 Round 4: 298 peptides, 28 chains. Longest chain 32 peptides. Score 0.537 Round 5: 297 peptides, 30 chains. Longest chain 22 peptides. Score 0.520 Taking the results from Round 4 Chains 30, Residues 270, Estimated correctness of the model 0.0 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 10076 reflections ( 99.70 % complete ) and 7991 restraints for refining 3734 atoms. 6831 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2772 (Rfree = 0.000) for 3734 atoms. Found 20 (20 requested) and removed 29 (10 requested) atoms. Cycle 37: After refmac, R = 0.2655 (Rfree = 0.000) for 3688 atoms. Found 20 (20 requested) and removed 23 (10 requested) atoms. Cycle 38: After refmac, R = 0.2565 (Rfree = 0.000) for 3661 atoms. Found 20 (20 requested) and removed 27 (10 requested) atoms. Cycle 39: After refmac, R = 0.2497 (Rfree = 0.000) for 3643 atoms. Found 16 (20 requested) and removed 19 (10 requested) atoms. Cycle 40: After refmac, R = 0.2485 (Rfree = 0.000) for 3628 atoms. Found 11 (20 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.70 2.75 Search for helices and strands: 0 residues in 0 chains, 3790 seeds are put forward NCS extension: 19 residues added (5 deleted due to clashes), 3809 seeds are put forward Round 1: 272 peptides, 39 chains. Longest chain 18 peptides. Score 0.409 Round 2: 295 peptides, 31 chains. Longest chain 24 peptides. Score 0.510 Round 3: 289 peptides, 30 chains. Longest chain 17 peptides. Score 0.508 Round 4: 282 peptides, 31 chains. Longest chain 19 peptides. Score 0.489 Round 5: 286 peptides, 32 chains. Longest chain 22 peptides. Score 0.488 Taking the results from Round 2 Chains 32, Residues 264, Estimated correctness of the model 0.0 % 4 chains (43 residues) have been docked in sequence ------------------------------------------------------ 10076 reflections ( 99.70 % complete ) and 7724 restraints for refining 3733 atoms. 6541 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2637 (Rfree = 0.000) for 3733 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 42: After refmac, R = 0.2441 (Rfree = 0.000) for 3714 atoms. Found 16 (20 requested) and removed 17 (10 requested) atoms. Cycle 43: After refmac, R = 0.2375 (Rfree = 0.000) for 3703 atoms. Found 16 (20 requested) and removed 18 (10 requested) atoms. Cycle 44: After refmac, R = 0.2311 (Rfree = 0.000) for 3677 atoms. Found 10 (20 requested) and removed 14 (10 requested) atoms. Cycle 45: After refmac, R = 0.2285 (Rfree = 0.000) for 3657 atoms. Found 14 (20 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.65 2.71 Search for helices and strands: 0 residues in 0 chains, 3834 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 3859 seeds are put forward Round 1: 257 peptides, 37 chains. Longest chain 19 peptides. Score 0.399 Round 2: 299 peptides, 34 chains. Longest chain 18 peptides. Score 0.494 Round 3: 288 peptides, 32 chains. Longest chain 16 peptides. Score 0.491 Round 4: 294 peptides, 32 chains. Longest chain 18 peptides. Score 0.501 Round 5: 286 peptides, 29 chains. Longest chain 20 peptides. Score 0.511 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 257, Estimated correctness of the model 0.0 % 2 chains (28 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2a2m-3_warpNtrace.pdb as input Building loops using Loopy2018 30 chains (257 residues) following loop building 2 chains (28 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10076 reflections ( 99.70 % complete ) and 7972 restraints for refining 3734 atoms. 6858 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2718 (Rfree = 0.000) for 3734 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2606 (Rfree = 0.000) for 3685 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2582 (Rfree = 0.000) for 3648 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2535 (Rfree = 0.000) for 3617 atoms. TimeTaking 257.88